Insights into Regulation of C₂ and C₄ Photosynthesis in Amaranthaceae/Chenopodiaceae Using RNA-Seq

Amaranthaceae (incl. Chenopodiaceae) shows an immense diversity of C₄ syndromes. More than 15 independent origins of C₄ photosynthesis, and the largest number of C₄ species in eudicots signify the importance of this angiosperm lineage in C₄ evolution. Here, we conduct RNA-Seq followed by comparative transcriptome analysis of three species from Camphorosmeae representing related clades with different photosynthetic types: Threlkeldia diffusa (C₃), Sedobassia sedoides (C₂), and Bassia prostrata (C₄). Results show that B. prostrata belongs to the NADP-ME type and core genes encoding for C₄ cycle are significantly upregulated when compared with Sed. sedoides and T. diffusa. Sedobassia sedoides and B. prostrata share a number of upregulated C₄-related genes; however, two C₄ transporters (DIT and TPT) are found significantly upregulated only in Sed. sedoides. Combined analysis of transcription factors (TFs) of the closely related lineages (Camphorosmeae and Salsoleae) revealed that no C₃-specific TFs are higher in C₂ species compared with C₄ species; instead, the C₂ species show their own set of upregulated TFs. Taken together, our study indicates that the hypothesis of the C₂ photosynthesis as a proxy towards C₄ photosynthesis is questionable in Sed. sedoides and more in favour of an independent evolutionary stable state.